Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

Follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL) are the two most common non-Hodgkin lymphomas (NHLs). Here we sequenced tumour and matched normal DNA from 13 DLBCL cases and one FL case to identify genes with mutations in B-cell NHL. We analysed RNA-seq data from these and another 113 NHLs to identify genes with candidate mutations, and then re-sequenced tumour and matched normal DNA from these cases to confirm 109 genes with multiple somatic mutations. Genes with roles in histone modification were frequent targets of somatic mutation. For example, 32% of DLBCL and 89% of FL cases had somatic mutations in MLL2, which encodes a histone methyltransferase, and 11.4% and 13.4% of DLBCL and FL cases, respectively, had mutations in MEF2B, a calcium-regulated gene that cooperates with CREBBP and EP300 in acetylating histones. Our analysis suggests a previously unappreciated disruption of chromatin biology in lymphomagenesis

Delayed diagnosis and issues with pump usage are the leading causes of diabetic ketoacidosis in children with diabetes living in Newfoundland and Labrador, Canada

Background Newfoundland and Labrador (NL) has a very high incidence of type 1 diabetes (T1DM) and admission rate for diabetic ketoacidosis (DKA). The purpose of this study was to identify characteristics and precipitating factors associated with pediatric DKA in this population. Methods This was a retrospective study on children diagnosed with DKA from 2007–2011 admitted to the province’s only tertiary care pediatric hospital. Demographics, biochemical characteristics, and reasons for DKA diagnosis were analyzed. Chi-square and Fisher Exact tests were performed for categorical variables; t- and non-parametric Kruskal-Wallis tests were performed for continuous variables. Results A total of 90 children were admitted with DKA (39.5% newly diagnosed; 60.5% were previously diagnosed). The rate of DKA on presentation for incident cases was 22.1%. More severe cases of DKA occurred in younger, newly diagnosed patients. Almost half of preexisting diabetes cases were recurrent DKA (49.1%). The most common presenting characteristics of newly diagnosed patients were weight loss, bedwetting, polyuria, polydipsia, and neurologic symptoms. Pre-existing diabetes patients most often presented with abdominal pain and vomiting. Diagnosis of diabetes in new patients and issues related to interrupted insulin delivery in pre-existing patients using insulin pump therapy were the most common factors associated with DKA. Of the newly diagnosed patients presenting in DKA, 64% had seen a physician in the weeks leading up to diagnosis. Conclusions Pediatric patients have predictable patterns associated with a diagnosis of DKA. Most cases of DKA could be prevented with earlier diagnosis and improved education and problem-solving by families and health care providers. DKA preventative strategies are recommended and should be aimed at patients, their families, and health care professionals especially those outside of pediatric centers

Assessing antifreeze activity of AFGP 8 using domain recognition software

Domain recognition software was employed to assess recrystallization-inhibition (RI) activity as an index of antifreeze potential. This represents a key step in the development of a high-throughput analysis for RI activity. Analysis of measurement error indicates an average coefficient of variation for individual crystals of about 8%, which is very small in relation to other sources of variation. Our analysis demonstrates an inverse correlation between AFGP 8 concentration and average crystal size with consistently small, but detectable differences in average crystal size at the edge and centre of the ice wafer. Sensitivity analysis using Monte Carlo re-sampling methods indicate that measuring of 12-15 crystals per field of view are sufficient to obtain accurate estimates of the first two moments (mean and variance) of the crystal size distribution, thereby greatly reducing the time required to assess recrystallization activity. These results suggest that this method has considerable potential for high-throughput analysis of RI activity.NRC publication: Ye

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers

Abstract Background The long-range sequencing information captured by linked reads, such as those available from 10× Genomics (10xG), helps resolve genome sequence repeats, and yields accurate and contiguous draft genome assemblies. We introduce ARKS, an alignment-free linked read genome scaffolding methodology that uses linked reads to organize genome assemblies further into contiguous drafts. Our approach departs from other read alignment-dependent linked read scaffolders, including our own (ARCS), and uses a kmer-based mapping approach. The kmer mapping strategy has several advantages over read alignment methods, including better usability and faster processing, as it precludes the need for input sequence formatting and draft sequence assembly indexing. The reliance on kmers instead of read alignments for pairing sequences relaxes the workflow requirements, and drastically reduces the run time. Results Here, we show how linked reads, when used in conjunction with Hi-C data for scaffolding, improve a draft human genome assembly of PacBio long-read data five-fold (baseline vs. ARKS NG50 = 4.6 vs. 23.1 Mbp, respectively). We also demonstrate how the method provides further improvements of a megabase-scale Supernova human genome assembly (NG50 = 14.74 Mbp vs. 25.94 Mbp before and after ARKS), which itself exclusively uses linked read data for assembly, with an execution speed six to nine times faster than competitive linked read scaffolders (~ 10.5 h compared to 75.7 h, on average). Following ARKS scaffolding of a human genome 10xG Supernova assembly (of cell line NA12878), fewer than 9 scaffolds cover each chromosome, except the largest (chromosome 1, n = 13). Conclusions ARKS uses a kmer mapping strategy instead of linked read alignments to record and associate the barcode information needed to order and orient draft assembly sequences. The simplified workflow, when compared to that of our initial implementation, ARCS, markedly improves run time performances on experimental human genome datasets. Furthermore, the novel distance estimator in ARKS utilizes barcoding information from linked reads to estimate gap sizes. It accomplishes this by modeling the relationship between known distances of a region within contigs and calculating associated Jaccard indices. ARKS has the potential to provide correct, chromosome-scale genome assemblies, promptly. We expect ARKS to have broad utility in helping refine draft genomes

Virtual Engagement of Families in the Intensive Care Unit During COVID-19: A Descriptive Survey of Family Members of Patients and Health Care Workers

Introduction: Traditional face-to-face family member visits in the intensive care unit (ICU) are challenged during the coronavirus disease pandemic with time-critical visiting of the ICU patient being impossible.Objective: This study aimed to explore reported experiences and satisfaction surrounding the use of technology for virtual visits and virtual family meetings in the ICU setting. Two groups were surveyed: (1) family members of critically ill patients in the ICU and (2) health care workers caring for these patients.Design: The study, conducted in the 36-bed ICU of a speciality metropolitan acute care facility in Australia, used a pragmatic post-test survey design. Data were analyzed descriptively.Results: Of health care worker subjects, 106 completed the survey and the majority of communication episodes favored virtual visits (79.2%, n = 84). Of family member subjects, 69 completed the survey, with the majority participating in virtual family meetings (40.6%, n = 28). Both groups indicated satisfaction with virtual communication.Conclusions: We found virtual communication was positively received

Maternal Obesity Reduces Milk Lipid Production in Lactating Mice by Inhibiting Acetyl-CoA Carboxylase and Impairing Fatty Acid Synthesis

<div><p>Maternal metabolic and nutrient trafficking adaptations to lactation differ among lean and obese mice fed a high fat (HF) diet. Obesity is thought to impair milk lipid production, in part, by decreasing trafficking of dietary and <i>de novo</i> synthesized lipids to the mammary gland. Here, we report that <i>de novo</i> lipogenesis regulatory mechanisms are disrupted in mammary glands of lactating HF-fed obese (HF-Ob) mice. HF feeding decreased the total levels of acetyl-CoA carboxylase-1 (ACC), and this effect was exacerbated in obese mice. The relative levels of phosphorylated (inactive) ACC, were elevated in the epithelium, and decreased in the adipose stroma, of mammary tissue from HF-Ob mice compared to those of HF-fed lean (HF-Ln) mice. Mammary gland levels of AMP-activated protein kinase (AMPK), which catalyzes formation of inactive ACC, were also selectively elevated in mammary glands of HF-Ob relative to HF-Ln dams or to low fat fed dams. These responses correlated with evidence of increased lipid retention in mammary adipose, and decreased lipid levels in mammary epithelial cells, of HF-Ob dams. Collectively, our data suggests that maternal obesity impairs milk lipid production, in part, by disrupting the balance of <i>de novo</i> lipid synthesis in the epithelial and adipose stromal compartments of mammary tissue through processes that appear to be related to increased mammary gland AMPK activity, ACC inhibition, and decreased fatty acid synthesis.</p></div

Additional file 1: of ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers

Table S1. Genomic data sources. Table S2. Summary of 10× Genomics Chromium datasets used for assemblies and scaffolding. Table S3. Summary of draft assemblies used for scaffolding with linked reads. Table S4. Contiguity and Quast summary of scaffolding a C. elegans Supernova assembly. Table S5. Contiguity and accuracy of scaffolding a Supernova assembly of the NA12878 individual. Table S6. Reconstruction of the human chromosomes in a baseline and ARKS-scaffolded NA12878 Supernova assembly. Table S7. Baseline ABySS NA24143 contig assembly metrics. Table S8. Contiguity and benchmarking analysis of scaffolding ABySS NA24143 contigs with ARKS. Table S9. Wall clock time and peak memory usage for scaffolding the Supernova C. elegans base assembly with ARKS, ARCS, fragScaff and Architect. Table S10. Wall clock time and peak memory usage for scaffolding the Supernova NA12878 draft assembly with ARKS, ARCS, fragScaff and Architect. Table S11. Wall clock time and peak memory usage for scaffolding the NA24143 Falcon+HiRise draft assembly with ARKS. Table S12. Assembly contiguity and breakpoint analysis of ARKS scaffolding of a Pacbio Falcon assembly scaffolded with Hi-C/HiRise. Figure S1. Gap size estimation in ARKS. Figure S2. ARKS gap distance estimation analysis. (PDF 446 kb

Effects of HF feeding and obesity on perilipin 2 levels in mammary glands of lactating dams.

<p>Perilipin 2 levels in mammary glands of LF-fed, HF-Ln and HF-Ob dams at L10. (A) Representative immunoblot images of Plin2 and β-actin in total mammary gland extracts. (B) Chemiluminescence quantification of Plin2 relative to β-actin in mammary gland extracts. The left (HF Feeding) panel compares relative Plin2 levels in mammary gland extracts of LF- and HF-fed dams. The right (Obesity) panel compares relative Plin2 levels in mammary gland extracts of HF-Ln and HF-Ob dams. The values are means ± SEM for Plin2 normalized to β-actin (N = 5). (C) Representative images of mammary gland sections from LF-Fed, HF-Ln and HF-Ob dams at L10 immunostained for Plin2 (green), Plin1 (red, to identify mammary adipose), and DAPI (blue, to identify nuclei). Boxed areas show regions of the mammary epithelium indicated by the white arrows at higher magnification. White arrowheads indicate Plin2 coated CLD in mammary epithelial cells. Yellow stars indicate regions of the mammary gland containing adipose. (D) Quantification of the effects of HF feeding and obesity on Plin2 immunofluorescence in the mammary epithelium. The left (HF Feeding) panel compares average relative Plin2 IF levels in mammary epithelium of LF- and HF-fed (HF-Ln and HF-Ob) dams. The right (Obesity) panel compares average relative Plin2 IF levels in mammary epithelium of HF-Ln and HF-Ob dams. Plin2 IF intensities in mammary alveoli were quantified in 5 randomly chosen sections from each animal and normalized to the percentage of gland within each section. The values are means ± SEM (N = 5). Statistically significant differences are indicate by the following symbols: *<i>p</i><0.05; ♦♦p<0.02.</p